neither ignition is really better out of the box. but the s13 ignition is technically better since it requires less modification when upgrading the coil and such (s14 requires a post to be installed in the dist. cap to make it external.

yeah dave is right on the valve cover, s13's have the 3 bolts that run down the center of the valve cover on the top, the s14 valve cover has the rearmost center bolt in the back.

obd2 s14 intake manifolds have 2 bolt castings on the front side of runner #1, obd1 s14s and s13s dont have as many castings, but if it's an s14 motor in s13, its likely the intake manifolds could have been swapped out to accomodate emissions devices.